| Previous changeset 2:4b14d0e3a837 (2014-04-14) Next changeset 4:077f404ae1bb (2017-06-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
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modified:
get_flanks.py get_flanks.xml tool_dependencies.xml |
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| diff -r 4b14d0e3a837 -r 4cd116158aef get_flanks.py --- a/get_flanks.py Mon Apr 14 09:18:30 2014 -0400 +++ b/get_flanks.py Wed Nov 11 12:48:31 2015 -0500 |
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| b'@@ -9,15 +9,17 @@\n -o, --off=N: Offset\n """\n \n-import sys, re, os\n+import sys\n from bx.cookbook import doc_optparse\n-from galaxy.tools.util.galaxyops import *\n+from galaxy.tools.util.galaxyops import parse_cols_arg\n+\n \n def stop_err( msg ):\n sys.stderr.write( msg )\n sys.exit()\n \n-def main(): \n+\n+def main():\n try:\n if int( sys.argv[3] ) < 0:\n raise Exception\n@@ -30,26 +32,26 @@\n chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )\n inp_file, out_file, size, direction, region = args\n if strand_col_1 <= 0:\n- strand = "+" #if strand is not defined, default it to +\n+ strand = "+" # if strand is not defined, default it to +\n except:\n stop_err( "Metadata issue, correct the metadata attributes by clicking on the pencil icon in the history item." )\n try:\n offset = int(options.off)\n size = int(size)\n- except: \n+ except:\n stop_err( "Invalid offset or length entered. Try again by entering valid integer values." )\n \n- fo = open(out_file,\'w\')\n- \n+ fo = open(out_file, \'w\')\n+\n skipped_lines = 0\n first_invalid_line = 0\n invalid_line = None\n elems = []\n- j=0\n+ j = 0\n for i, line in enumerate( file( inp_file ) ):\n line = line.strip()\n if line and (not line.startswith( \'#\' )) and line != \'\':\n- j+=1\n+ j += 1\n try:\n elems = line.split(\'\\t\')\n #if the start and/or end columns are not numbers, skip that line.\n@@ -76,15 +78,15 @@\n elems[end_col_1] = str(int(elems[start_col_1]) + size)\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- \n+\n elif direction == \'Downstream\':\n if strand == \'-\':\n if region == \'start\':\n- elems[end_col_1] = str(int(elems[end_col_1]) - offset)\n- elems[start_col_1] = str( int(elems[end_col_1]) - size )\n+ elems[end_col_1] = str(int(elems[end_col_1]) - offset)\n+ elems[start_col_1] = str( int(elems[end_col_1]) - size )\n else:\n- elems[end_col_1] = str(int(elems[start_col_1]) - offset)\n- elems[start_col_1] = str( int(elems[end_col_1]) - size )\n+ elems[end_col_1] = str(int(elems[start_col_1]) - offset)\n+ elems[start_col_1] = str( int(elems[end_col_1]) - size )\n elif strand == \'+\':\n if region == \'start\':\n elems[start_col_1] = str(int(elems[start_col_1]) + offset)\n@@ -94,31 +96,31 @@\n elems[end_col_1] = str(int(elems[start_col_1]) + size)\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- \n+\n elif direction == \'Both\':\n if strand == \'-\':\n if region == \'start\':\n start = str(int(elems[end_col_1]) - offset)\n end1 = str(int(start) + size)\n end2 = str(int(start) - size)\n- elems[start_col_1]=start\n- elems[end_col_1]=end1\n+ elems[start_col_1] = start\n+ elems[end_col_1] = end1\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- elems[start_col_1]=end2\n- elems[end_col_1]=start\n+ '..b' fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- elems[start_col_1]=end2\n- elems[end_col_1]=start2\n+ elems[start_col_1] = end2\n+ elems[end_col_1] = start2\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n elif strand == \'+\':\n@@ -139,24 +141,24 @@\n start = str(int(elems[start_col_1]) + offset)\n end1 = str(int(start) - size)\n end2 = str(int(start) + size)\n- elems[start_col_1]=end1\n- elems[end_col_1]=start\n+ elems[start_col_1] = end1\n+ elems[end_col_1] = start\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- elems[start_col_1]=start\n- elems[end_col_1]=end2\n+ elems[start_col_1] = start\n+ elems[end_col_1] = end2\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n elif region == \'end\':\n start = str(int(elems[end_col_1]) + offset)\n end1 = str(int(start) - size)\n end2 = str(int(start) + size)\n- elems[start_col_1]=end1\n- elems[end_col_1]=start\n+ elems[start_col_1] = end1\n+ elems[end_col_1] = start\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- elems[start_col_1]=start\n- elems[end_col_1]=end2\n+ elems[start_col_1] = start\n+ elems[end_col_1] = end2\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n else:\n@@ -164,12 +166,12 @@\n end1 = str(int(start1) - size)\n start2 = str(int(elems[end_col_1]) + offset)\n end2 = str(int(start2) + size)\n- elems[start_col_1]=end1\n- elems[end_col_1]=start1\n+ elems[start_col_1] = end1\n+ elems[end_col_1] = start1\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n- elems[start_col_1]=start2\n- elems[end_col_1]=end2\n+ elems[start_col_1] = start2\n+ elems[end_col_1] = end2\n assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0\n fo.write( "%s\\n" % \'\\t\'.join( elems ) )\n except:\n@@ -183,7 +185,7 @@\n stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )\n if skipped_lines > 0:\n print \'Skipped %d invalid lines starting with #%dL "%s"\' % ( skipped_lines, first_invalid_line, invalid_line )\n- print \'Location: %s, Region: %s, Flank-length: %d, Offset: %d \' %( direction, region, size, offset )\n- \n+ print \'Location: %s, Region: %s, Flank-length: %d, Offset: %d \' % ( direction, region, size, offset )\n+\n if __name__ == "__main__":\n main()\n' |
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| diff -r 4b14d0e3a837 -r 4cd116158aef get_flanks.xml --- a/get_flanks.xml Mon Apr 14 09:18:30 2014 -0400 +++ b/get_flanks.xml Wed Nov 11 12:48:31 2015 -0500 |
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| @@ -17,8 +17,8 @@ <option value="Downstream">Downstream</option> <option value="Both">Both</option> </param> - <param name="offset" size="10" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/> - <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/> + <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/> + <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/> </inputs> |
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| diff -r 4b14d0e3a837 -r 4cd116158aef tool_dependencies.xml --- a/tool_dependencies.xml Mon Apr 14 09:18:30 2014 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:48:31 2015 -0500 |
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| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="bx-python" version="0.7.1"> - <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2d0c08728bca" name="package_bx_python_0_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="galaxy-ops" version="1.0.0"> - <repository changeset_revision="4e39032e4ec6" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9cbb20b85c01" name="package_galaxy_ops_1_0_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |